Illumina Infinium Genotyping
The Infinium assay from Illumina allows whole genome genotyping at different levels of coverage, using a variety of fixed content chips. A few of the more recently released chips are the MEGA, Human Omni5, HumanOmni2.5-8, OmniExpress, and the Exome-targeted chip for genotyping and copy number analysis. The Translational Genomics Core at Partners Personalized Medicine is happy to offer any chips currently available from Illumina, including the newest chips detailed at Illumina’s website.
Custom genotyping of large numbers of SNPs also is available, using the iSelect system. Several standard chips allow the addition of iSelect custom SNP sets to allow customization of the chip for the researchers specific aims. The Infinium iSelect allows researchers to interrogate up to 60k custom SNPS.
The latest Infinium assay is a PCR independent assay. Whole genome amplification is followed by hybridization of the loci of interest to 50-mer probes, stopping one base before the interrogated marker. Single base extension is then carried out to incorporate a labeled nucleotide. Dual color (red/green) staining allows the nucleotide to be detected by the iSCAN reader and is converted to genotype during analysis with the GenomeStudio analysis software.
Raw data is delivered via our LIMS (GIGPAD) and is in the form of a .csv file which connects sample ID with marker ID and genotype.
|Sample type||Minimum quantity||Concentration||Buffer||Container||Controls|
|Genomic DNA||20 ul||50 ng/ul by picogreen; 75-100 ng/ul if quantitated by other methods||TE buffer (10 mM Tris, ph7.5: 1 mM EDTA)||Full-skirted 96-well plate||Leave well H12 empty for internal control DNA. We recommend including duplicate samples as controls.|
All DNA plates delivered to the lab for Genotyping will be quantitated by picogreen to ensure the concentration of the DNA is at the required 50 ng/ul. Those samples with lower concentrations or high amounts of degradation will only be genotyped with permission from the principal investigator with the understanding that Partners Personalized Medicine is not responsible for drop in data quality. If concentrations are greater than required by the technology, then we are able to normalize the concentration in-house for a charge, or the plates can be returned to the customer for normalization. Please note that normalization will increase turn-around time. You may waive the option of quality control (QC), but then no guarantee is given to the quality of the genotypes, and all costs will be passed onto the customer regardless of quality of data. WGA DNA is not recommended due to decreased call rate and amplification of allelic bias present in the original WGA sample.
Each batch of 95 samples will be genotyped alongside a positive control sample. The resulting genotypes from the positive control sample will be compared over time to ensure reproducibility and performance of our lab process.
SNP sequences for iSelect Assay design
Submit biallelic SNPs to PPMCore@partners.org as rs numbers or sequence.
We work on a first-come, first- served basis. Our expected turn-around time depends on our queue at the time we receive your samples. Once receiving the reagents, processing takes 2–3 weeks for up to 5 plates. Larger projects may require additional processing time.